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Hello Usman--
>
> I get a .pdb file with the oxygen atoms and hydrogen atoms completely
> separated. I thought the topology file allows for bonds between two
> hydrogens and oxygen atom..
you might try changing
this part
>
> {* a structure with randomly distributed coordinates *}
> coor fractional end
> vector do (x=random()) ( all ) {* Generate fake coordinates *}
> vector do (y=random()) ( all ) {* to avoid error messages *}
> vector do (z=random()) ( all ) {* about unknown atoms. *}
> coord orthogonal
> end
>
to
coor fractional end
vector do (x=random()) ( name O* ) {* Generate fake
coordinates *}
vector do (y=random()) ( name O* ) {* to avoid error messages
*}
vector do (z=random()) ( name O* ) {* about unknown atoms.
*}
coord orthogonal
flags exclude vdw elec end {*Do hydrogen building w/o vdw*}
{*and elec. *}
hbuild {*This statement builds missing*}
selection=( hydrogen ) {*hydrogens, which are needed *}
phistep=45 {*for the force field. *}
end
constraints fix=( not hydrogen ) end {* Minimize hydrogen positions. *}
flags include vdw elec end
minimize powell
nstep=40
end
constraints fix=( not all ) end
minimize powell
nstep=1000
end
end
Charles
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